PDA Data in Thermo Raw File Prevents Skyline Import

PDA Data in Thermo Raw File Prevents Skyline Import ddrruss  2024-01-31 08:44

I am using the most recent version of skyline, on a windows 10 OS.

I have a PDA detector inline and am collecting UV as well as MS1 and MS2 (DDA using a thermo ascend).
I am using a byonic mzid file to build my library.
When I try to upload my raw file I get an error that says something along the lines of PDA chromatogram not recognized. It looks like Skyline is also trying to import the PDA data from my raw file in addition to the mass spec data. I can send the raw data file for inspection.

Nick Shulman responded:  2024-01-31 14:57
Yes, if you send us your files we can try to figure out what is going on.

It would be helpful if you would send us both your Skyline document and your .raw file.
In Skyline you can use the menu item:
File > Share
to create a .zip file containing your Skyline document and supporting files.

If that .zip file and/or your .raw file are less than 50MB you can attach them to this support request.
You can upload larger files here:

-- Nick
ddrruss responded:  2024-02-01 10:42
Hi Nick,.

Thank you, I uploaded relevent files as a folder. The file name is 240201 and attached to my user name "ddrruss". Files uploaded to the larger file uploaded section,.


Nick Shulman responded:  2024-02-01 11:43
Thanks for sending those files.
It looks like there is a bug in Skyline and msconvert which causes an error when trying to read "EE_Neat2.raw".
I think you can work around this bug by telling msconvert.exe to skip over all the chromatograms.

That is, you would run it with a command-line like:
msconvert.exe EE_Neat2.raw --chromatogramFilter "index 1000"

Those arguments
--chromatogramFilter "index 1000"
tell msconvert.exe to only include the 1000th chromatogram, which does not exist, so it has the effect of removing all of the chromatograms from the resulting .mzML file.

I will try to find someone to fix the error that happens when you try to use the .raw file normally.
-- Nick
ddrruss responded:  2024-02-01 12:25
Hi Nick,

Thank you for quickly looking into this. Let me know if someone can patch Skyline to accommodate raw files with the PDA data. Is there a command line option within Skyline that I can paste that line? I am not used to interacting with this software outside of its GUI.


Nick Shulman responded:  2024-02-01 13:08
In order to get "msconvert.exe" you should install ProteoWizard:

If you install ProteoWizard for "All Users" then it will be installed somewhere under "C:\Program Files\ProteoWizard". (If you install it just for yourself it will be installed somewhere deep under your AppData and will be difficult to find so it's easiest if you install it for "all users").

You will then need to run msconvert.exe from the commandline yourself to convert your .raw file to .mzML and tell it to discard all the chromatograms.

Note that when you install ProteoWizard, you do get something on the Start Menu called MSConvert, but that starts a program called MSConvertGUI.exe which does not have an option to exclude chromatograms. If you have to use MSConvertGUI.exe, you could tell it to create a .mzXML file instead of a .mzML file, and that would also have the effect of excluding the chromatograms because .mzXML is an old format that does not support chromatograms at all.
-- Nick
Nick Shulman responded:  2024-02-06 16:21

We believe your raw file is actually corrupted and that is the reason that ProteoWizard and Skyline cannot read it without error.

We also get an error using Thermo QualBrowser to look at the file.

In general, you can work around errors like this in msconvert.exe by including "--continueOnError" on the commandline.

I imagine that if you have other files in the same dataset, these other files would work just fine in Skyline and QualBrowser. If that turns out not to be the case, and you see errors in QualBrowser then you might need to contact Thermo for a fix.
-- Nick